4YWJ | pdb_00004ywj

Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa

• PDB DOI: https://doi.org/10.2210/pdb4YWJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-20 Released: 2015-04-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 4-hydroxy-tetrahydrodipicolinate reductase (HTPA reductase) from Pseudomonas aeruginosa

Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.63 kDa 
• Atom Count: 4,411 
• Modeled Residue Count: 536 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A, B	276	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: dapB, PA4759 EC: 1.17.1.8
UniProt
Find proteins for P38103 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P38103  Go to UniProtKB:  P38103

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], G [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
PGE	D [auth A], H [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
BU1	E [auth A], I [auth B]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34YWJ

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.01	α = 90
b = 101.5	β = 90
c = 144.51	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
ARP	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-04-01
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy